Here is an example of setting up NT mode for ISDN2.

In system.conf
# Span 3: BRI/0/2 "PIKA BRI_TE Module A Span 1" AMI/CCS
Note the addition of the 'nt' and 'term' values.
Also the second parameter denotes the clock. Normally NT provides clock so this value is set to 0.

Once you have configured your ports run dahdi_cfg -vvv